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        <title>Profile Editor Window</title>
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        <h1 align="center">Profile Editor Window</h1>
		<p align="left">
		<b><a name="Fc plot"></a>The Fc plot:</b></p>
		<p align="left">
		The top panel presents a plot of the amplification profile (Fc vs. cycle 
		number). The actual 
		fluorescence readings (Fc) are displayed as dots, with the predicted Fc 
		displayed as circles and the
		<a href="../lre_window_selection/window_definition.html">LRE window</a> 
		as red circles (used for linear regression analysis as described below) .</p>
		<p align="center">
		<img border="0" src="images/fc_plot.gif" width="360" height="112"></p>
		<p align="left">
		C<sub>1/2</sub> 
		is the fraction cycle at which reaction fluorescence 
		reaches half of it maximum, Fmax, and defines profile position similar 
		to Cq. Fb and Fb slope are the background fluorescence and baseline 
		slope, respectively, derived from
		<a href="../nonlinear_regression/nr.htm">nonlinear regression analysis</a>. The line spanning the 
		upper region of the profile is the run&#39;s average Fmax, that is, the 
		average Fmax generated by all of the profiles within the run. In 
		addition to defining the fluorescence scale generated by the run, the average Fmax 
		also 
		provides the foundation for
		<a href="../fmax_normalize/fmax_normalization.htm">Fmax Normalization</a>. </p>
		
    	<p align="left"><b><a name="LRE Plot"></a>The LRE plot:</b></p>
		<p align="left">The LRE plot generates a linear representation of the 
		profile amplification kinetics, with the C<sub>1/2 </sub>denoted by the red dot. Produced by 
		plotting <a href="../glossary/glossary.html#Cycle_Efficiency">cycle efficiency</a> (E<sub>C</sub>) against 
		cycle fluorescence 
		(F<sub>C</sub>), linear regression analysis provides values 
		for the amplification efficiency (<a href="../glossary/glossary.html#Emax">Emax</a>) from the Y-intercept, and the 
		rate of loss in amplification efficiency (<a href="../glossary/glossary.html#deltaE">ΔE</a>) from the slope, using 
		the cycles within the <a href="../glossary/glossary.html#LRE_Window">LRE window</a> denoted by the 
		red circles. This process, referred to as &quot;<a href="../glossary/glossary.html#LRE_Analysis">LRE analysis</a>&quot;, 
		from which target quantity is determined in fluorescence units (F<sub>0</sub>) 
		(see below). </p>
		<p align="center">
		<img border="0" src="images/lre_plot.gif" width="360" height="210"></p>
		<p align="left">This panel also allows the LRE window to be 
		manually adjusted by clicking on the ±Cycle buttons. The left buttons 
		increase or reduce the bottom of the LRE window by one cycle, whereas 
		the right buttons increase or reduce the top of the LRE window by one 
		cycle. The &quot;Reset&quot; button re-implements automated 
		LRE window selection.
		</p>
		<p align="left">A more detailed description of LRE window selections is provided in the
		<a href="../lre_window_selection/lre_window_selection_overview.html">LRE 
		window selection</a> section.&nbsp; </p>
		<p align="left"><b><a name="Fo Plot"></a>The F<sub>0</sub> Plot:</b></p>
		<p align="center">
		<img border="0" src="images/fo_plot.gif" width="259" height="109"></p>
		<p align="left">The F<sub>0</sub> plot provides a visual illustration of 
		how target quantity is determined directly 
		from the F<sub>C</sub> values generated by each of the cycles within the LRE 
		window (red circles). This is accomplished using a derivative of the classic Boltzmann sigmoid equation 
		that has been adapted to PCR amplification in which target quantity is 
		expressed in fluorescence units:</p>
		<p align="center">
		<img border="0" src="images/equation1.gif" width="243" height="73"></p>
		<p align="left">Depending on the size of the LRE window, this produces 4-8 determinations 
		from which an average F<sub>0</sub> is calculated, which, in combination 
		with the amplicon size and an <a href="../glossary/glossary.html#OCF">optical calibration factor</a>, is 
		used to calculate the number of target molecules. </p>
		<p align="left"><b><a name="Tsble Summary"></a>The Table Summary</b>:</p>
		<p align="center">
		<img border="0" src="images/table.gif" width="257" height="209"></p>
		<p align="left">This table provides a numerical summary for cycles 
		encompassing the LRE window (denoted in red in the last column). The 
		cycle fluorescence (F<sub>C</sub>), cycle efficiency (<a href="../glossary/glossary.html#Cycle_Efficiency">E<sub>C</sub></a>) and the percent of the 
		average F<sub>0</sub> are presented for each cycle. Combined with the F<sub>C</sub> 
		plot, this provides insights into the kinetics of amplification within 
		the profile, along with the level of conformity to the
		<a href="../glossary/glossary.html#LRE_Model">LRE model</a>. The
		<a href="../lre_window_selection/lre_window_selection_overview.html">LRE 
		Window Selection</a> section provides additional details about the %Av. 
		Fo and how this is used to automate selection the upper limit of the LRE 
		window. </p>
		<p align="left">Although a more detailed description is beyond the scope 
		of this introduction, it may be worthwhile to expand further on two of 
		the most important insights provided by this summary. </p>
		<p align="left">The first is that contrary to the widely held belief 
		that amplification efficiency is constant, at least in the lower region 
		of an amplification profile, amplification efficiency as reflected by 
		the cycle efficiency is clearly not constant. Instead, this reveals that 
		a substantive loss in amplification efficiency occurs even within the 
		earliest cycles of an amplification profile. </p>
		<p align="left">The second is particularly significant for those 
		unfamiliar with LRE, which is illustration of the process 
		underpinning LRE quantification, which is the conversion of fluorescence 
		readings (F<sub>C</sub>) into target quantity expressed in fluorescence units (F<sub>0</sub>). 
		In this example, the generated F<sub>0</sub> values differ from the average by up 
		to 1.29%, over a range of F<sub>C</sub> readings that increase by almost 
		10X.</p>
		<p align="left"><b><a name="Data Info Panel"></a>The Data Information Panel:</b></p>
		<p align="center">
		<img border="0" src="images/lre_object_info.gif" width="360" height="312"></p>
		<p align="left">This panel displays and allows editing of 
		information about the selected data element. In this example, a 
		replicate profile has been selected, which in addition to general 
		information such as the name of the amplicon and sample, presents the 
		well label and amplicon Tm of the selected profile. </p>
		<p align="left">Note that the type of information will change when a 
		different type of data element is selected. For example, when a run is selected, 
		only its name and notes are presented. Note also that most of this 
		information can be edited, which, for example, allows addition of notes 
		to any element, or in this case, the ability to change the amplicon size 
		or the strandedness of the target, both of which will change the 
		predicted target quantity.</p>
    	<p align="left"><b><a name="Window Selection Parameters"></a>The LRE Window Selection Parameters</b></p>
		<p align="center">
		<img border="0" src="images/lre_window_parameters.gif" width="255" height="114"></p>
		<p align="left">This final panel, which is located in the top right, 
		provides the ability to manually adjust the automated LRE window 
		selection parameters. A more detailed description is provided in the
		<a href="../lre_window_selection/lre_window_selection_overview.html">LRE 
		Window Selection</a>. </p>
    	<p align="left"><b><a name="NR Panel"></a>The Nonlinear Regression Panel</b></p>
		<p align="left">This panel lists the parametric values derived from nonlinear 
		regression analysis, conducted via a reiterative process in which the 
		analysis is repeated 3X, from which an average and CV are determined for 
		each parameter. </p>
		<p align="center">
		<img border="0" src="images/nr_panel.gif" width="250" height="129"></p>
		<p align="left">Note, however, that only Fb and Fb-slope are actually 
		used in the LRE analysis. Values for the other three parameters are 
		only provided for reference. </p>
		<p align="left">Those interested in a more detailed 
		description of how nonlinear regression was implemented should contact 
		the author via RGRutledge@gmail.com.</p>
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